20230207 - fix check build warnings/errors

Author: isaactpetersen

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: petersenlab
 Type: Package
 Title: Package of R Functions for the Petersen Lab
-Version: 0.1.2-9014
+Version: 0.1.2-9015
 Authors@R: person("Isaac T.", "Petersen",
   email = "isaac-t-petersen@uiowa.edu",
   role = c("aut", "cre"), 

NAMESPACE

@@ -70,7 +70,6 @@ export(write.aes)
 importFrom(Hmisc,rcorr)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(digest,AES)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
@@ -115,14 +114,24 @@ importFrom(psych,corr.p)
 importFrom(psych,partial.r)
 importFrom(reshape2,melt)
 importFrom(stats,anova)
+importFrom(stats,as.formula)
+importFrom(stats,coef)
+importFrom(stats,cor)
+importFrom(stats,cor.test)
 importFrom(stats,density)
 importFrom(stats,lm)
 importFrom(stats,lm.influence)
+importFrom(stats,loess)
 importFrom(stats,loess.control)
+importFrom(stats,logLik)
+importFrom(stats,median)
+importFrom(stats,na.exclude)
 importFrom(stats,na.omit)
+importFrom(stats,pchisq)
 importFrom(stats,pnorm)
 importFrom(stats,ppoints)
 importFrom(stats,predict)
+importFrom(stats,pt)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,resid)

R/accuracyAtCutoff.R

@@ -78,7 +78,7 @@
 #'
 #' @family accuracy
 #'
-#' @importFrom dplyr %>% mutate group_by summarise
+#' @importFrom dplyr mutate group_by summarise
 #' @importFrom ggplot2 cut_number
 #' @importFrom stringr str_replace_all str_split
 #' @importFrom stats qnorm na.omit
@@ -169,8 +169,8 @@ accuracyAtCutoff <- function(predicted, actual, cutoff, UH = NULL, UM = NULL, UC
 
     bin <- NULL
 
-    calibrationTable <- mutate(data, bin = cut_number(predicted, n = bins)) %>%
-      group_by(bin) %>%
+    calibrationTable <- mutate(data, bin = cut_number(predicted, n = bins)) |>
+      group_by(bin) |>
       summarise(n = length(predicted),
                 meanPredicted = mean(predicted, na.rm = TRUE),
                 meanObserved = mean(actual, na.rm = TRUE),

R/addCorrelationToScatterplot.R

@@ -28,7 +28,7 @@
 #' @family correlations
 #'
 #' @importFrom graphics text
-#' @importFrom stats na.omit
+#' @importFrom stats na.omit median cor.test
 #'
 #' @export
 #'

R/equivalenceTest.R

@@ -23,6 +23,8 @@
 #' @return p-value indicating whether to reject the null hypothesis that the
 #' model is a poor fit to the data.
 #'
+#' @importFrom stats pchisq
+#'
 #' @export
 #'
 #' @examples

R/hlm.R

@@ -18,6 +18,7 @@
 #' @family mixedModel
 #'
 #' @importFrom nlme lme intervals getResponse
+#' @importFrom stats cor
 #'
 #' @export
 #'

R/imputationCombine.R

@@ -17,7 +17,7 @@
 #'
 #' @importFrom nlme fixef
 #' @importFrom mix mi.inference
-#' @importFrom stats na.omit
+#' @importFrom stats na.omit cor
 #'
 #' @export
 #'

R/imputationModelCompare.R

@@ -19,6 +19,8 @@
 #'
 #' @family multipleImputation
 #'
+#' @importFrom stats logLik
+#'
 #' @export
 #'
 #' @examples

R/lmCombine.R

@@ -16,7 +16,7 @@
 #' @family multipleImputation
 #'
 #' @importFrom mix mi.inference
-#' @importFrom stats vcov lm
+#' @importFrom stats vcov lm coef
 #'
 #' @export
 #'

R/make_esem_model.R

@@ -24,7 +24,7 @@
 #'
 #' @family lavaan
 #'
-#' @importFrom dplyr %>% filter select rename
+#' @importFrom dplyr filter select rename
 #' @importFrom lavaan sem parameterEstimates
 #'
 #' @export
@@ -65,10 +65,10 @@
 #' esem_loadings <- lavaan::parameterEstimates(
 #'   efa_fit,
 #'   standardized = TRUE
-#' ) %>%
-#'   filter(efa == "efa1") %>%
-#'   select(lhs, rhs, est) %>%
-#'   rename(item = rhs, latent = lhs, loading = est)
+#' ) |>
+#'   dplyr::filter(efa == "efa1") |>
+#'   dplyr::select(lhs, rhs, est) |>
+#'   dplyr::rename(item = rhs, latent = lhs, loading = est)
 #'
 #' # Specify Anchor Item for Each Latent Factor
 #' anchors <- c(f1 = "x3", f2 = "x5", f3 = "x7")